Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Gene Value Type Rank description Interaction Map network_comparison Network Comparison Type Filtered red green
Results: HTML CSV LaTeX Showing element 1 to 50 of 19268 in total
Value Type  : Measured
Rank
description
Interaction Map
network_comparison
Network Comparison Type
Filtered
red
green
1 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] High confidence 6325 Subtracted 0 85 6410
Low confidence
carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] 8870.5 1 40899 32028.5
lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] 4.4149 Divided 2399.5 543.5
mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] High confidence 8126 Subtracted 41482.5 33356.5
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 36400000 Divided 0 364 0.00001
Low confidence
rad50-interacting protein 1. [refseq;acc:nm_021930] High confidence 5.31521 1 450.5 2394.5
2 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Low confidence 7307 Subtracted 21185 28492
cab2. [refseq;acc:nm_033419] High confidence 17400000 Divided 0 0.00001 174
cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] Low confidence 4.4149 1 2399.5 543.5
cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] High confidence 8126 Subtracted 41482.5 33356.5
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Low confidence 8900000 Divided 0 0.00001 89
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] High confidence 6325 Subtracted 85 6410
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Low confidence 4196.8 23818.1 19621.3
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] High confidence 5.31521 Divided 1 450.5 2394.5
3 cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] Low confidence 4.4149 2399.5 543.5
cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] High confidence 8126 Subtracted 41482.5 33356.5
homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 3.71868 Divided 2597.5 698.5
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Low confidence 8900000 0 0.00001 89
mitochondrial solute carrier protein. [refseq;acc:nm_145305] 7307 Subtracted 1 21185 28492
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] High confidence 4196.8 0 23818.1 19621.3
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] Low confidence 2393.82 5106.93 7500.75
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] High confidence 10900000 Divided 0.00001 109
4 anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801] Low confidence 2274 Subtracted 2082 4356
bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090] 7035.1 1 36474.3 43509.4
cytohesin 4. [swissprot;acc:q9uia0] High confidence 8126 41482.5 33356.5
hbs1-like. [refseq;acc:nm_006620] 3.71868 Divided 2597.5 698.5
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Low confidence 8900000 0 0.00001 89
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] High confidence
lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] Low confidence 4.4149 1 2399.5 543.5
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] High confidence 3026 Subtracted 0 18704 21730
5 cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 8126 1 41482.5 33356.5
histone h4. [swissprot;acc:p02304] 2673.2 0 21773.1 24446.3
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 8900000 Divided 0.00001 89
jumonji protein. [swissprot;acc:q92833] Low confidence 1751660 17.5166
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] High confidence 3.39764 1 1153.5 339.5
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] Low confidence 2254.84 Subtracted 0 485.286 2740.13
oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] 2.86965 Divided 1 736.5 2113.5
vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] 7034 Subtracted 36469.3 43503.3
6 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] High confidence 8900000 Divided 0 0.00001 89
homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099] Low confidence 1300000 13 0.00001
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] High confidence 3.39764 1 1153.5 339.5
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Low confidence 7008.5 Subtracted 36360.3 43368.8
oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [swissprot;acc:q9h4l5] 2.86965 Divided 736.5 2113.5
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] High confidence 7563 Subtracted 44490.5 36927.5
similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] 2430.4 0 13174.7 15605.1
Low confidence 1244.48 7592.37 8836.85
7 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] High confidence 7307 1 21185 28492
cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] Low confidence 1238.62 0 4660.09 5898.71

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/